IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-39632-w.html
   My bibliography  Save this article

Cell cycle arrest and p53 prevent ON-target megabase-scale rearrangements induced by CRISPR-Cas9

Author

Listed:
  • G. Cullot

    (Bordeaux University, INSERM, BRIC, U1312)

  • J. Boutin

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Biochemistry Laboratory)

  • S. Fayet

    (Bordeaux University, INSERM, BRIC, U1312)

  • F. Prat

    (Bordeaux University, INSERM, BRIC, U1312)

  • J. Rosier

    (Bordeaux University, INSERM, BRIC, U1312)

  • D. Cappellen

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Tumor Biology and Tumor Bank Laboratory)

  • I. Lamrissi

    (Bordeaux University, INSERM, BRIC, U1312)

  • P. Pennamen

    (CHU de Bordeaux, department of medical genetics)

  • J. Bouron

    (CHU de Bordeaux, department of medical genetics)

  • S. Amintas

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Tumor Biology and Tumor Bank Laboratory)

  • C. Thibault

    (Bordeaux University, INSERM, BRIC, U1312)

  • I. Moranvillier

    (Bordeaux University, INSERM, BRIC, U1312)

  • E. Laharanne

    (CHU de Bordeaux, Tumor Biology and Tumor Bank Laboratory)

  • J. P. Merlio

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Tumor Biology and Tumor Bank Laboratory)

  • V. Guyonnet-Duperat

    (Bordeaux University, INSERM, BRIC, U1312
    Vect’UB, vectorology platform, INSERM US 005—CNRS UAR 3427-TBM-Core, Bordeaux university)

  • J. M. Blouin

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Biochemistry Laboratory)

  • E. Richard

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Biochemistry Laboratory)

  • S. Dabernat

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Biochemistry Laboratory)

  • F. Moreau-Gaudry

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Biochemistry Laboratory)

  • A. Bedel

    (Bordeaux University, INSERM, BRIC, U1312
    CHU de Bordeaux, Biochemistry Laboratory)

Abstract

The CRISPR-Cas9 system has revolutionized our ability to precisely modify the genome and has led to gene editing in clinical applications. Comprehensive analysis of gene editing products at the targeted cut-site has revealed a complex spectrum of outcomes. ON-target genotoxicity is underestimated with standard PCR-based methods and necessitates appropriate and more sensitive detection methods. Here, we present two complementary Fluorescence-Assisted Megabase-scale Rearrangements Detection (FAMReD) systems that enable the detection, quantification, and cell sorting of edited cells with megabase-scale loss of heterozygosity (LOH). These tools reveal rare complex chromosomal rearrangements caused by Cas9-nuclease and show that LOH frequency depends on cell division rate during editing and p53 status. Cell cycle arrest during editing suppresses the occurrence of LOH without compromising editing. These data are confirmed in human stem/progenitor cells, suggesting that clinical trials should consider p53 status and cell proliferation rate during editing to limit this risk by designing safer protocols.

Suggested Citation

  • G. Cullot & J. Boutin & S. Fayet & F. Prat & J. Rosier & D. Cappellen & I. Lamrissi & P. Pennamen & J. Bouron & S. Amintas & C. Thibault & I. Moranvillier & E. Laharanne & J. P. Merlio & V. Guyonnet-D, 2023. "Cell cycle arrest and p53 prevent ON-target megabase-scale rearrangements induced by CRISPR-Cas9," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39632-w
    DOI: 10.1038/s41467-023-39632-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-39632-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-39632-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Fatwa Adikusuma & Sandra Piltz & Mark A. Corbett & Michelle Turvey & Shaun R. McColl & Karla J. Helbig & Michael R. Beard & James Hughes & Richard T. Pomerantz & Paul Q. Thomas, 2018. "Large deletions induced by Cas9 cleavage," Nature, Nature, vol. 560(7717), pages 8-9, August.
    2. Michael Kosicki & Felicity Allen & Frances Steward & Kärt Tomberg & Yangyang Pan & Allan Bradley, 2022. "Cas9-induced large deletions and small indels are controlled in a convergent fashion," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Stamatis Papathanasiou & Styliani Markoulaki & Logan J. Blaine & Mitchell L. Leibowitz & Cheng-Zhong Zhang & Rudolf Jaenisch & David Pellman, 2021. "Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing," Nature Communications, Nature, vol. 12(1), pages 1-7, December.
    4. J. Boutin & J. Rosier & D. Cappellen & F. Prat & J. Toutain & P. Pennamen & J. Bouron & C. Rooryck & J. P. Merlio & I. Lamrissi-Garcia & G. Cullot & S. Amintas & V. Guyonnet-Duperat & C. Ged & J. M. B, 2021. "CRISPR-Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    5. Grégoire Cullot & Julian Boutin & Jérôme Toutain & Florence Prat & Perrine Pennamen & Caroline Rooryck & Martin Teichmann & Emilie Rousseau & Isabelle Lamrissi-Garcia & Véronique Guyonnet-Duperat & Al, 2019. "CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    6. Ha Youn Shin & Chaochen Wang & Hye Kyung Lee & Kyung Hyun Yoo & Xianke Zeng & Tyler Kuhns & Chul Min Yang & Teresa Mohr & Chengyu Liu & Lothar Hennighausen, 2017. "CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome," Nature Communications, Nature, vol. 8(1), pages 1-10, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Jianli Tao & Daniel E. Bauer & Roberto Chiarle, 2023. "Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Burcu Bestas & Sandra Wimberger & Dmitrii Degtev & Alexandra Madsen & Antje K. Rottner & Fredrik Karlsson & Sergey Naumenko & Megan Callahan & Julia Liz Touza & Margherita Francescatto & Carl Ivar Möl, 2023. "A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Jianhang Yin & Kailun Fang & Yanxia Gao & Liqiong Ou & Shaopeng Yuan & Changchang Xin & Weiwei Wu & Wei-wei Wu & Jiaxu Hong & Hui Yang & Jiazhi Hu, 2022. "Safeguarding genome integrity during gene-editing therapy in a mouse model of age-related macular degeneration," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    4. Michael Kosicki & Felicity Allen & Frances Steward & Kärt Tomberg & Yangyang Pan & Allan Bradley, 2022. "Cas9-induced large deletions and small indels are controlled in a convergent fashion," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Jianli Tao & Qi Wang & Carlos Mendez-Dorantes & Kathleen H. Burns & Roberto Chiarle, 2022. "Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Ju-Chan Park & Yun-Jeong Kim & Gue-Ho Hwang & Chan Young Kang & Sangsu Bae & Hyuk-Jin Cha, 2024. "Enhancing genome editing in hPSCs through dual inhibition of DNA damage response and repair pathways," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    7. Dan Liang & Aleksei Mikhalchenko & Hong Ma & Nuria Marti Gutierrez & Tailai Chen & Yeonmi Lee & Sang-Wook Park & Rebecca Tippner-Hedges & Amy Koski & Hayley Darby & Ying Li & Crystal Dyken & Han Zhao , 2023. "Limitations of gene editing assessments in human preimplantation embryos," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    8. Jianhang Yin & Rusen Lu & Changchang Xin & Yuhong Wang & Xinyu Ling & Dong Li & Weiwei Zhang & Mengzhu Liu & Wutao Xie & Lingyun Kong & Wen Si & Ping Wei & Bingbing Xiao & Hsiang-Ying Lee & Tao Liu & , 2022. "Cas9 exo-endonuclease eliminates chromosomal translocations during genome editing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    9. M. Kyle Cromer & Valentin V. Barsan & Erich Jaeger & Mengchi Wang & Jessica P. Hampton & Feng Chen & Drew Kennedy & Jenny Xiao & Irina Khrebtukova & Ana Granat & Tiffany Truong & Matthew H. Porteus, 2022. "Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    10. Hsiu-Hui Tsai & Hsiao-Jung Kao & Ming-Wei Kuo & Chin-Hsien Lin & Chun-Min Chang & Yi-Yin Chen & Hsiao-Huei Chen & Pui-Yan Kwok & Alice L. Yu & John Yu, 2023. "Whole genomic analysis reveals atypical non-homologous off-target large structural variants induced by CRISPR-Cas9-mediated genome editing," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    11. Jun Huang & David Rowe & Pratima Subedi & Wei Zhang & Tyler Suelter & Barbara Valent & David E. Cook, 2022. "CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    12. Lukas Möller & Eric J. Aird & Markus S. Schröder & Lena Kobel & Lucas Kissling & Lilly van de Venn & Jacob E. Corn, 2022. "Recursive Editing improves homology-directed repair through retargeting of undesired outcomes," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    13. Martin Peterka & Nina Akrap & Songyuan Li & Sandra Wimberger & Pei-Pei Hsieh & Dmitrii Degtev & Burcu Bestas & Jack Barr & Stijn Plassche & Patricia Mendoza-Garcia & Saša Šviković & Grzegorz Sienski &, 2022. "Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    14. Stamatis Papathanasiou & Styliani Markoulaki & Logan J. Blaine & Mitchell L. Leibowitz & Cheng-Zhong Zhang & Rudolf Jaenisch & David Pellman, 2021. "Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing," Nature Communications, Nature, vol. 12(1), pages 1-7, December.
    15. Panagiotis Antoniou & Giulia Hardouin & Pierre Martinucci & Giacomo Frati & Tristan Felix & Anne Chalumeau & Letizia Fontana & Jeanne Martin & Cecile Masson & Megane Brusson & Giulia Maule & Marion Ro, 2022. "Base-editing-mediated dissection of a γ-globin cis-regulatory element for the therapeutic reactivation of fetal hemoglobin expression," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    16. Sanju Sinha & Karina Barbosa & Kuoyuan Cheng & Mark D. M. Leiserson & Prashant Jain & Anagha Deshpande & David M. Wilson & Bríd M. Ryan & Ji Luo & Ze’ev A. Ronai & Joo Sang Lee & Aniruddha J. Deshpand, 2021. "A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    17. Hye Kyung Lee & Michaela Willi & Chengyu Liu & Lothar Hennighausen, 2023. "Cell-specific and shared regulatory elements control a multigene locus active in mammary and salivary glands," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    18. Behrouz Eslami-Mossallam & Misha Klein & Constantijn V. D. Smagt & Koen V. D. Sanden & Stephen K. Jones & John A. Hawkins & Ilya J. Finkelstein & Martin Depken, 2022. "A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    19. Sebald A. N. Verkuijl & Estela Gonzalez & Ming Li & Joshua X. D. Ang & Nikolay P. Kandul & Michelle A. E. Anderson & Omar S. Akbari & Michael B. Bonsall & Luke Alphey, 2022. "A CRISPR endonuclease gene drive reveals distinct mechanisms of inheritance bias," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    20. Zhiqian Li & Lang You & Anita Hermann & Ethan Bier, 2024. "Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39632-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.